Evidence for the plant recruitment of beneficial microbes ... · 31/07/2020 · 4 Hongwei Liu1, 2, Jiayu Li1, Lilia C. Cavalhais3, Cassandra Percy4, Jay Prakash Verma5, Peer 5 M

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Evidence for the plant recruitment of beneficial microbes to suppress soil-borne 1 pathogen 2

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Hongwei Liu1, 2, Jiayu Li1, Lilia C. Cavalhais3, Cassandra Percy4, Jay Prakash Verma5, Peer 4

M. Schenk2,7, Brajesh Singh1,6,7* 5

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1Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2753, 7

Australia; 2School of Agriculture and Food Sciences, The University of Queensland, Saint 8

Lucia, Queensland 4072, Australia; 3Centre for Horticultural Science, Queensland Alliance 9

for Agriculture and Food Innovation, The University of Queensland, Saint Lucia, 10

Queensland 4102 Australia; 4Centre for crop health, University of Southern Queensland, 11

Toowoomba, Queensland 4350, Australia; 5Institute of Environment and Sustainable 12

Development, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India; 6Global 13

Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW 2753, 14

Australia. 7These authors contributed equally. 15

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*Corresponding author: [email protected] 17

(which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprintthis version posted August 1, 2020. ; https://doi.org/10.1101/2020.07.31.231886doi: bioRxiv preprint

https://doi.org/10.1101/2020.07.31.231886

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Summary 18

• Emerging experimental framework suggests that plants under biotic stress may actively 19

seek help from soil microbes, but empirical evidence underlying such a ‘cry for help’ 20

strategy is limited. 21

• We used integrated microbial community profiling, pathogen and plant transcriptive 22

gene quantification and culture-based methods to systematically investigate a three-way 23

interaction between the wheat plant, wheat-associated microbiomes and Fusarium 24

pseudograminearum (Fp). 25

• A clear enrichment of a dominant bacterium, Stenotrophomonas rhizophila (SR80), was 26

observed in both the rhizosphere and root endosphere of Fp-infected wheat. SR80 27

reached 3.7×107 cells g-1 in the rhizosphere and accounted for up to 11.4% of the 28

microbes in the root endosphere. Its abundance had a positive linear correlation with 29

the pathogen load at base stems and expression of multiple defense genes in top leaves. 30

Upon re-introduction in soils, SR80 enhanced plant growth, both the below- and above-31

ground, and induced strong disease resistance by priming plant defense in the 32

aboveground plant parts, but only when the pathogen was present 33

• Together, the bacterium SR80 seems to have acted as an early warning system for plant 34

defense. This work provides novel evidence for the potential protection of plants against 35

pathogens by an enriched beneficial microbe via modulation of the plant immune 36

system. 37

Key words: crown rot; endophytes; Fusarium pseudograminearum; plant microbiome; 38

Stenotrophomonas rhizophila; wheat. 39

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Introduction 41

Plants have been subject to selective pressures from pathogens, pests, and undesirable soil 42

(e.g., nutrient deficient) and weather (e.g., drought) conditions since their evolutionary origin 43

(Chakraborty & Newton, 2011; Liu et al., 2019). Assemblages of host-specific microbiomes 44

in the rhizosphere, root endosphere and other niches, such as the phyllosphere (leaf) and 45


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anthosphere (flower) have been reported (Edwards et al., 2015; Álvarez-Pérez et al., 2019; 46

Grady et al., 2019). Emerging evidence indicates that these microbial symbionts, rather than 47

merely acting as tenants, intimately interact with plants and influence their immune systems 48

and multiple processes of plant growth and development (Liu et al., 2019). However, 49

detailed mechanistic evidence for these interactions is missing and how these hugely diverse 50

commensal microbes interact with plants is largely unknown. Addressing these knowledge 51

gaps is urged to support future translational research for the application of microbe-based 52

products in sustainable agriculture. 53

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The rhizosphere is a hotspot for plant-soil-microbe and microbe-microbe interactions. The 55

microbes and their interactions can largely prevent pathogen outgrowth and extend the plant 56

capacity for disease resistance (Durán et al., 2018). Recent studies revealed that some 57

disease-resistant crop varieties (e.g. tomato and common bean) enrich particular sets of 58

bacterial species in the rhizosphere to suppress pathogens (Kwak et al., 2018; Mendes et al., 59

2018). This suggests that specific soil microbes/microbial functions contribute to protection 60

against plant diseases. Furthermore, it has been shown that diseased plants significantly 61

promoted specific beneficial microbes in their associated microbiomes, which could act as 62

an extended layer of plant defense and a legacy to enhance survival rates of their offspring 63

(Berendsen et al., 2018). However, whether the rhizosphere and root endophytic microbiota 64

are coordinated to modulate plant-pathogen interactions and plant performance is unknown. 65

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Recent theoretical framework of co-evolution also suggests that recruitment of beneficial 67

microbes upon biotic stress is likely a survival strategy conserved across the plant kingdom 68

although empirical evidence is still scarce and mechanistic pathways remain poorly defined 69

(Liu & Brettell, 2019; Liu et al., 2019). Whether such a cry for help strategy applies to crop- 70

pathogen interactions in field conditions is unknown. Moreover, plants differ in physiology 71

and immune response to pathogen invasions, meaning mechanisms are likely to be plant 72

species-dependent. In this study, we investigated interactions between durum wheat 73


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(Triticum turgidum var. durum) and its microbial symbionts in the rhizosphere and root 74

endosphere upon infection with the fungal pathogen Fusarium pseudograminearum (Fp). 75

Crown rot (CR) disease caused by Fp is a devastating soil-borne disease, which can infect 76

winter cereal crops of all stages and lead to large losses in global cereal production 77

(estimated at $79 million/year in Australia alone) (Akinsanmi et al., 2004). However, so far, 78

there are no CR-resistant crop varieties and effective control through chemical fungicides is 79

currently not available. Using wheat-Fp system, we aimed to explore responses of plant 80

microbiomes to pathogen infection and identify mechanisms underpinning plant-microbiome 81

interactions that may mediate disease resistance of the plant. 82

83

In an effort to achieve our aims, durum wheat plants were sampled from a field experiment 84

where Fp inoculations have been historically occurring at the Queensland Department of 85

Agriculture and Fisheries (DAF) research farm at Wellcamp (Australia). Soil and tissues 86

from symptomatic plants that were naturally infected with Fp were collected, along with 87

those from asymptomatic plants, to identify key microbial taxa in the plant microbiome that 88

are associated with plant defense responses. We profiled microbial communities in the 89

rhizosphere and roots using bacterial and fungal amplicon sequencing. Plant defense status 90

was evaluated by determining the transcript abundances of defense genes involved in the 91

salicylic acid (SA) and jasmonic acid (JA) signaling pathways. Bacteria were then isolated 92

from Fp-infected plants and effects of a disease-enriched bacterium on durum wheat defense 93

and growth were investigated in glasshouse experiments. 94

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Methods and Materials 96

Fp treatments in field experiments and sampling 97

Field samples were collected from a wheat trial conducted in 2015 at the Queensland 98

Department of Agriculture and Fisheries (DAF) Experimental Farm at Wellcamp 99

(27°33'54.7"S, 151°51'52.0"E), Queensland, Australia. The soil is a black Vertosol with 100

chemical properties listed in Table S1. Farm management histories including past yield trials, 101


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CR trials and fallow periods are shown in Table S2. Plus and minus Fp (the causal agent for 102

CR disease) inoculated yield plots (6 m x 2 m) were sown in a randomized complete block 103

design in June 2015. Colonized millet grain inoculum (Percy et al., 2012) was applied in the 104

furrow in a band above the seed at planting. Experimental plots were surrounded by a 7-row 105

buffer zone (2 m each) of non-inoculated durum wheat (Jandaroi variety), running 150 m 106

along the length of the experiment. CR was observed in many plants in the non-inoculated 107

Jandaroi buffer during tillering and as jointing progressed. Diseased plants were scattered 108

amongst asymptomatic plants. Fp-infected plant residues remaining from a previous CR 109

experiment (2010) may have been retained in the field and continued to provide a source of 110

inoculum to infect subsequent hosts. The research presented in this study compares samples 111

taken from plants that were asymptomatic and symptomatic for CR in Jandaroi buffer rows, 112

as we aimed to investigate plants naturally infected with Fp. 113

114

Thirteen weeks after sowing, both healthy and infected plants were carefully uprooted using 115

a shovel and separated into independent individuals from three different locations of the field 116

in September 2015. Forty healthy and 18 infected plants were collected for microbiome 117

analyses. The top ~10 cm of two to three leaves were cut, transferred into a 15 mL Falcon 118

tube and immediately frozen in dry ice. The leaf along with stem and root (soil attached) 119

samples were stored in dry ice and transported to the laboratory on the same day and 120

preserved at -80°C. Approximately 5 grams of fresh roots (rhizosphere soil attached) 121

collected from a Fp-infected plant were kept at 4°C until microbial isolation. 122

123

Processing of the rhizosphere soil and root samples 124

Stems, roots and soils were separated before further processing. The procedures included 125

three steps. (i) The most basal internode/base stem (~5 cm that covers an area of brown 126

discoloration of each plant) was cut and scored for disease levels following the protocol 127

below. The stem samples were ground into a fine powder in liquid nitrogen and stored at -128

80°C for DNA extraction. (ii) Bulk soil was removed from roots by shaking them vigorously. 129


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(iii) Rhizosphere soil was then separated from roots by shaking root and soil in 25 mL 130

0.1�M sterile phosphate buffer (7.1�g Na2HPO4, 4.4�g NaH2PO4·H2O added to 820�mL 131

deionized water, pH 7.0) in a 50 mL plastic conical centrifuge tube at 200 rpm for 5 min. 132

Roots were then transferred to a new tube for subsequent procedures. The soil suspension 133

was centrifuged at 4,000 g for 15 min and the obtained soil pellet was regarded as the 134

rhizosphere soil and stored at -80°C until genomic DNA extraction. Roots were thoroughly 135

washed under distilled water, followed by surface sterilization to remove microbes on the 136

surface by shaking roots in 25 mL of 4% sodium hypochlorite solution at 200 rpm for 5 min. 137

The roots were then washed three times with sterile phosphate buffer. The last wash was 138

inoculated on a nutrient agar plate incubated for 2 days at 37°C and no viable colonies 139

formed, which indicated that the disinfection procedure was efficient. Roots were air-dried in 140

a laminar hood and stored at -80°C until grinding step in liquid nitrogen leading to a fine 141

powder for DNA extraction. 142

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Disease scoring 144

CR was rated based on the percentage of brown discoloration at the stem base using a 0 to 4 145

scale previously reported (Wildermuth & McNamara, 1994). A score of 0 indicates no 146

visible discoloration, and a score of 1, 2, 3, and 4 describe discoloration of 0~25%, 26% to 147

50%, 51%~75% and 76%~100%, respectively. 148

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DNA extraction from soil and plant samples 150

Genomic DNA (gDNA) was extracted from about 0.2 g plant (stem or root) samples using a 151

Maxwell® 16 LEV Plant DNA Kit on a Maxwell® 16 Instrument (AS2000) according to the 152

manufacturer’s instructions. Soil gDNA was extracted from 0.25 g soil per sample using the 153

PowerSoilTM DNA Isolation kit (MO BIO Laboratories, Carlsbad, CA) as per the 154

manufacturer’s recommendations. Plant and soil DNA concentrations were determined using 155

a QubitTM fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen). The DNA samples 156

were stored at -20°C until further analysis. 157


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158

Fp and total fungi quantification 159

Fp and total fungi colonizing the plant and soil samples were quantified using qPCR. The 160

details of the qPCR system and thermal conditions are described in the Supplementary 161

Materials of this study. The proportion of Fp/total fungi DNA to wheat DNA was counted as 162

the relative abundance of Fp/fungi in wheat plants (Melloy et al., 2010). Fp and fungi were 163

estimated using (i) the Tri5 gene from the trichothecene cluster responsible for trichothecene 164

production of Fusarium species, and (ii) the fungal ribosomal 18S rRNA gene, respectively 165

(Melloy et al., 2010). Wheat actin-binding protein coding sequence was used as the 166

reference gene (Table S3). Quantification of these genes was performed using SYBR Green 167

on a ViiA™ 7 sequence detection system (Applied Biosystems, USA) with two replications 168

for each sample. Amplification specificity for each gene was examined by running melt 169

curve analysis, and the Fp amounts were then estimated according to 170

171

Relative Biomass= 172

where Ef is PCR amplification efficiency, which was calculated by LinRegPCR 7.5 based on 173

raw PCR amplification data (Ramakers et al., 2003). The relative abundance of Fp in soil 174

was also calculated, by comparing Ct values of each sample against a standard curve that 175

was generated by qPCRs using serially diluted Tri5 amplicons. 176

177

Quantification of defense-related genes in the leaf 178

RNA was isolated from ground leaf samples using Maxwell® 16 Total RNA Purification 179

(Promega) kit on an automated Maxwell® 16 Instrument as per the manufacturer’s 180

recommendations. RNA concentrations were quantified using a QubitTM fluorometer 181

(Invitrogen). cDNA was then synthesized from 2.5 μg RNA in a 20 μL reaction using both 182

random hexamers and oligo(dT) primers provided with the Tetro cDNA Synthesis kit 183

(BiolineTM). Ten defense genes were quantified using the SYBR Green qRT-PCR kit on a 184

ViiA™ 7 sequence detection system. These genes are marker genes for JA and SA signaling 185

EfFungal−Ct

EfPlant−Ct


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pathways, characterized in our previous study (Table S3) (Liu et al., 2016). The 18S rRNA 186

gene was used as the housekeeping gene for normalization, and the cDNA was diluted to 1: 187

500 before the amplification of this gene. The reverse transcriptase qPCR (qRT-PCR) 188

system and thermal conditions are described in the Supplementary Materials. 189

190

Plant and soil microbial community profiling using amplicon sequencing 191

The universal primers 926F (Engelbrektson et al., 2010) and 1392R (Peiffer et al., 2013) 192

were used for the amplification of bacterial and archaeal 16S rRNA genes in soil samples 193

(Table S3). The primers 799F and 1193R that preferentially amplify archaeal and bacterial 194

DNA in plant materials were used to amplify root endophytic microbes (Table S3). B 195

adaptor was linked to a key (TCAG) and connected to the above template-specific forward 196

primers. A adaptor was linked to a key sequence (TCAG) and a sample-specific molecular 197

identifier, and was then connected to a template-specific reverse primer (Table S3). 198

Amplifications were performed in duplicates for each sample and combined, using the PCR 199

system and conditions described in the Supplementary Materials. PCR products were 200

examined using agarose gel electrophoresis, and microbial amplification products for root 201

DNA samples were recovered from gels to remove the plant mitochondrial DNA-derived 202

amplicons which co-amplify using the 799F and 1193R primers but are of a different length. 203

The obtained 16S rRNA amplicons (~400�bp) were purified using Agencourt AMPure XP 204

beads (Beckman Coulter, Inc.) and quantified with a PicoGreen dsDNA Quantification Kit 205

(Invitrogen). Amplicons were then dual indexed using the Nextera XT Index Kit (Illumina) 206

according to the manufacturer’s instructions. Equal concentrations of each indexed sample 207

were pooled and sequenced on an Illumina MiSeq as per the manufacturer’s instructions at 208

the University of Queensland’s Institute for Molecular Biosciences (UQ, IMB). Additionally, 209

the fungal amplicon sequencing for soil samples was performed at the Western Sydney 210

University using the primer sets FITS7 (Ihrmark et al., 2012) and ITS4 (Glass & Donaldson, 211

1995) as per the standard MiSeq sequencing procedures. Bioinformatic analyses are 212

described in the Supplementary Materials of this study. 213


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214

Bacterial isolation 215

One gram of roots combined with rhizosphere soil from Fp-infected wheat were cut into 216

small pieces and homogenized with autoclaved glass beads (710-1180 µm, Sigma) in a 2 mL 217

centrifuge tube for 3 min using a TissueLyzer (Qiagen). The obtained mixture was serially 218

diluted in 5.0 mL sterile phosphate buffer and 150 µL aliquots of 10-4 to 10-7 dilutions were 219

spread onto plates containing a range of media: nutrient agar (NA), Pikovskaya’s agar, 220

tryptophan soy agar, King’s B agar and Stenotrophomonas spp. selective medium (32 mg L-1 221

Imipenem added, Adooq Biosciences) (Bollet et al., 1995). Plates were incubated at 30°C in 222

an incubator (Thermoline Scientific) for 2-5 days. Bacterial colonies were then picked based 223

on morphology, color and margin, and further purified by streaking on new NA plates. 224

Purified strains were stored in 25% glycerol at -80°C and sub-cultured on NA plates for the 225

required analyses. 226

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Antifungal assays 228

Fp strains CS3427, CS3321, CS3096 (Chakraborty et al., 2010) and A11 (strain in the field 229

trial) were used for this assay. They were cultured on potato dextrose agar (PDA) to a whole 230

plate size, and a mycelial plug of each fungus was placed in the center of a dual media plate 231

(½ PDA and ½ NA media). Tested bacteria were streaked at four ends of the plate and 232

cultured at 28°C for 7 days to examine antagonistic effects on these Fp strains. Two 233

Burkholderia bacterial strains were used as positive controls, and three replicates were 234

performed for the assay. Plates that inoculated with Fp only served as negative controls. 235

236

Bacterial identification and whole genome sequencing of SR80 237

Bacterial strains were identified based on their 16S rRNA gene sequence. They were 238

cultured in nutrient broth for 24 h, pelleted by centrifugation, washed and re-pelleted in PBS 239

buffer twice. Bacteria were then subjected to gDNA extraction using the DNeasy PowerSoil 240

Pro kit (Qiagen). A region of the 16S rRNA gene was amplified using 27F and 1492R 241


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primers (Table S3) and sequenced on a capillary sequencer at the Hawkesbury Institute for 242

the Environment (HIE). Sequences were quality-checked, trimmed and BLAST-searched 243

against the nucleotide database of NCBI using Geneious 10.1.3. Sequences of 244

Stenotrophomonas isolates were deposited in the NCBI database under GenBank accession 245

numbers MT151295 to MT151301. The identification of different Stenotrophomonas spp. 246

was further examined by BOX-PCR (for conditions see Supplementary Materials). 247

Sequences of other bacterial isolates are available under MT158490-MTI158578. Whole 248

genome sequencing of SR80 was conducted using the Illumina MiSeq platform by 249

Guangzhou Magigene Technology Co., Ltd. Sequencing success and quality were checked 250

with FastQC (0.11.8). A total of 11,331,006 high quality reads (Q>35) were obtained. De 251

novo assembling for high quality scaffolds was performed using SPAdes v3.9.0 (Nurk et al., 252

2017). The assembled sequences were deposited in the NCBI database under GenBank 253

accession number SAMN14299480. Hereafter, the components of coding genes, non-coding 254

RNA (ncRNA), and functional annotation using a range of databases including NR, 255

Swissprot, COG, KEGG, GO were performed. A circular map of the genome was obtained 256

using Circos version 0.69 (Krzywinski et al., 2009). The prediction of non-encoding 23S 257

rRNA and 16S rRNA were performed using rRNAmmer 1.2 (Lagesen et al., 2007). 258

259

Glasshouse experiments to assess effects of SR80 on wheat growth and defense 260

The biological relevance of SR80 on wheat was investigated in glasshouse experiments. The 261

soil used for wheat cultivation was collected from the Wellcamp site in August 2019 and 262

autoclaved twice to ensure Fp elimination. Three treatments including Fp only, SR80 only, 263

Fp & SR80, and control were applied in pot experiments at sowing time (8×12 cm pots, 264

approx. 200 g soil each). The Fp inoculum grown on whole wheat grain was developed 265

using the strain Fp A11#04, which was ground, sieved (2 mm) and stored in low humidity at 266

4°C until use. Fp was applied using an inoculation method modified from Wildermuth and 267

McNamara, 1994 (Fig.S1). Briefly, six Jandaroi seeds were sown in soil and covered with a 268

thin layer of soil, and topped by a layer of the Fp inoculant (1.0 g) in the form of fine powder. 269


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For treatments that excluded Fp, the autoclaved Fp inoculant was applied to reproduce the 270

chemical environment but the pathogen was not present in a living form. For bacterial 271

treatments, 40 mL of the SR80 suspension (in 50 μM PBS buffer, pH 7.0, OD600=1.0) was 272

inoculated to each pot, which provided ~2.4×108 SR80 cells g-1 bulk soil. As control, the 273

same amount of PBS buffer was added to treatment groups that excluded bacterial 274

inoculations. Soils in pots were then watered to field capacity to allow seeds to germinate. 275

Thereafter, soil was watered daily. The height of seedlings that emerged 3 days after sowing 276

was recorded twice daily (10 am and 4 pm) for 15 days. Disease and plant survival rates 277

were recorded once per day. The diameter of the stem base was recorded on the 7th and 14th 278

day after seedling emergence. Approx. 1.5 g of bulk soil was collected from the soil surface 279

from each pot at the 5th, 10th and 15th day for determining the abundances of SR80 and Fp. 280

When harvested, wheat shoots were cut, weighed, wrapped in aluminum foil and stored at -281

80°C for total RNA extraction. Roots were carefully separated from soils, thoroughly rinsed 282

with tap water, air-dried on paper tissues and weighed. Due to total lethality of plants in the 283

Fp-treated control group, an additional experiment was conducted, which included the Fp 284

and Fp+SR80 treatments using the same method as above but with a lower inoculant load 285

per pot (0.6 g). This provided sufficient plant material for RNA extractions and qRT-PCR 286

analyses. 287

288

Statistical analyses 289

Statistical analyses were implemented in R3.6.1. Linear model (Pearson correlation) was 290

performed using the package ggpubr (0.1.6) to determine (i) correlations of defense gene 291

abundance with disease severity, and (ii) correlations of SR80 abundance in soil and roots 292

with Fp amounts in plants. Data transformation was performed where needed to ensure data 293

normalization before conducting statistical analyses. The effects of Fp and SR80 on 294

responses of soil and plant microbial communities were investigated by permutational 295

multivariate analysis of variance (PERMANOVA) using Hellinger transformed OTU 296

abundances. This analysis was performed using the package vegan 2.5-6 (Dixon, 2003). 297


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Treatment effects on wheat growth, defense gene expression, alpha diversity of microbial 298

communities, and the abundance of SR80 and Fp were analyzed using one-way ANOVA 299

and Tukey post hoc tests. 300

301

Results 302

Plants were naturally infected by Fp and defense signaling pathways were activated in the 303

field study 304

Fifty-eight plants were collected from a field trial at the Wellcamp site. Symptomatology 305

inspections revealed that 40 of these plants were asymptomatic for CR and 18 plants 306

exhibited CR symptoms at different severity levels (Fig.1a). Disease severity of all plants 307

was visually rated based on discoloration of the stem and the level of Fp infection was 308

quantified by real-time quantitative polymerase chain reaction (qPCR) targeting the Tri5 309

gene (Fig.1b). The two methods provided consistent results (Fig.1b), as plants with visible 310

CR symptoms also had higher pathogen load quantified by qPCR (relative abundance ≥1) 311

than the asymptomatic plants (Fig.1a). Moreover, Fp load had a linear correlation with the 312

total fungi in base stem tissues (Fig.S2), indicating that Fp was the main component driving 313

the increases of fungal abundance in CR-infected plants in the field. Genes involved in plant 314

defense signaling pathways including PR2 (a beta-1,3-endoglucanase), PR3 (a chitinase), 315

PR4a (wheatwin), PR5 (a thaumatin-like protein), PR10 (a wheat peroxidase), TaPAL 316

(phenylalanine ammonia lyase) and Lipase were highly expressed in top leaves of Fp-317

infected plants (Fig.1c-j). These genes are known to be markers for the activation of JA 318

and/or SA signaling pathways in wheat (Liu et al., 2016). A positive linear correlation was 319

observed between transcript abundances of these defense genes and Fp load in the stem 320

tissues (Fig.1c-j, m&n). In contrast, the expression of two genes, TaNPR1 (wheat 321

nonexpressor of pathogenesis-related genes 1) and WCI3 (a sulfur-rich/thionin-like protein), 322

were not influenced by Fp (Fig.1k&l). Collectively, JA and SA defense signaling pathways 323

were activated in wheat by Fp (Fig.1m&n), which indicates successful progression of CR 324

and activation of plant defenses in the field. 325


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326

Microbiome structure differed between healthy and diseased wheat 327

Wheat roots seem to have acted as a barrier to select soil microbes, resulting in phylogenetic 328

conservation in the rhizosphere and root endosphere (Fig.S3a). These root-associated 329

compartments selected microbial phylotypes within the Proteobacteria, Actinobacteria and to 330

a lesser extent Bacteroidetes and Firmicutes while Acidobacteria, Gemmatimonadetes and 331

Archaea were almost depleted from the root endosphere (Fig.S3a). Meanwhile, a gradient 332

decrease of alpha diversty (e.g. observed species) from bulk soil to the root was observed 333

(Fig.S3b). However, no differences were seen in the alpha diversity for the rhizosphere and 334

root endosphere microbial communities between the healthy and diseased plants (Table S4). 335

336

The microbial composition in the rhizosphere of Fp-infected plants significantly differed 337

from that of healthy plants (PERMANOVA, P=0.0002) and were marginally different in the 338

root endosphere (P=0.073) (Fig.2a&b). Furthermore, the rhizosphere soil fungal community 339

composition significantly differed between healthy and diseased plants (P=0.001) (Fig.S4). 340

In the redundancy analyses for the rhizoshere communities (RDA, Fig.2a), bacterial OTU 341

89589 is strongly correlated with the Fp-infected plants and is one of the major dominant 342

OTUs in the separation of the diseased plants from healthy plants in the primary axis of the 343

RDA (RDA1), well separated from rest of the OTUs. A consistent pattern was also found in 344

the root endosphere, where OTU 41442 was among the most discriminating OTUs for 345

infected plants (Fig.2b). Further analyses revealed that these two OTUs had 100% nucleotide 346

similarity within the 16S rRNA region amplified, indicating that they were the same 347

bacterial strain (Fig.S5a, b), and belonged to Stenotrophomonas spp. 348

349

Further analyses revealed that the abundance of OTU 89589 (in the rhizosphere) positively 350

correlated to the Fp load in the stem tissues of infected plants (relative abundance ≥ 1) 351

(Fig.2c). This was less noticeable in asymptomatic plants (relative abundance <1) (Fig.2c). 352

Fp infection had contributed to the enrichment of this bacterium to as much as 3.7×107 cells 353


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per gram of the rhizosphere soil (Fig.2c). Similarly, the abundance of this bacterium in the 354

root endosphere also positively correlated with Fp abundance, accounting for up to 11.4% of 355

the bacterial community in roots (Fig.2d). These results suggest that the wheat-associated 356

microbiome had significantly changed in composition in response to Fp-infection, and 357

specifically enriched for a Stenotrophomonas spp. in the process. We also observed that 358

selection for the bacterium seems to have occurred even when wheat plants were healthy 359

(Fig.2e). Interestingly, the abundance of this bacterium also positively correlated with 360

transcript abundances of all PR defense genes tested (Fig.2f), suggesting that the bacterium 361

is likely to have contributed to the activation of plant defenses in the field. 362

363

Bacterial isolation, identification and whole genome sequencing 364

We attempted to isolate Stenotrophomonas spp., to investigate its biological implications on 365

wheat performance via controlled in vivo and in vitro tests. A total of 179 bacterial isolates 366

were recovered from the Fp-infected plant rhizosphere and roots using different media, 367

including a selective medium for Stenotrophomonas spp. Among these, seven isolates were 368

identified as Stenotrophomonas spp. by 16S rRNA Sanger sequencing, and these belonged to 369

four different strains (identified using BOX PCRs, Fig.S5a,b,c). Amplicon sequencing data 370

also revealed that different Stenotrophomonas species/strains (OTUs) colonized the 371

rhizosphere and roots, which is in line with the multiple strains obtained by the culture-372

dependent method. Among the four strains, only the 16S rRNA of Stenotrophomonas spp. 373

R80 (hereafter referred as SR80) had 100% nucleotide similarity match with the sequences of 374

OTU 89589 and OTU 41442 (Fig.S5a,b,c). The whole genome of SR80 was then sequenced 375

and analyzed (Fig.S6&7), through which the 16S rRNA region was obtained, which was 376

1,532 bp in length and had 100% sequence similarity to OTU 89589 and OTU 41442 377

(Fig.S6a,b). This suggests that SR80 was the bacterium enriched in the wheat microbiome by 378

Fp-infection (Fig.3a,b,c,d, Fig.S6a,b). The SR80 genome had the highest percent of Average 379

Nucleotide Identity (ANI) (97.71%) to a Stenotrophomonas rhizophila strain QL-P4 that was 380


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isolated from a pine tree leaf, suggesting it is a member of S.rhizophila species but possibly a 381

different strain. 382

383

The predicted genome size of SR80 is 4,234,260 bp containing 3,720 detected genes 384

(Fig.S7). Class of genes (COG) annotation was performed on the whole genome and 3,052 385

protein sequences were successfully annotated. Known virulence factors and plant cell wall 386

degrading enzymes were absent, but genes encoding proteins involved in symbiosis, host-387

cell interaction and activation of plant defense signaling pathways were detected. Genes 388

coding for bacterial flagellin (flg22), chitin (AvrXa21), and Type I~ Type IV secretion 389

systems were detected (Fig.S8), as were genes fliR and flhB which code for effector proteins 390

that interact with the plant immune system and induce the plant’s primary responses. Genes 391

encoding proteins involved in biofilm formation, chemotaxis, lipopolysaccharide (LPS) 392

biosynthesis, the quorum sensing system and reactive oxygen species (ROS) scavenging 393

(e.g., superoxide dismutase) are also present in multiple copies. These indicate that (i) SR80 394

can cope with plant immune responses that may prevent bacterial colonization, and (ii) this 395

bacterium could be well adapted to the root environment. SR80 was further studied in 396

antifungal tests against four virulent Fp strains (including the Fp used in the field experiment) 397

on dual media, but no noticeable inhibition was observed (Fig.3c). 398

SR80 promoted plant growth and defense 399

To evaluate whether SR80 affects wheat growth and defense, we treated the Fp-infected 400

variety of durum wheat (Jandaroi) with SR80 in glasshouse experiments (Fig.4). Overall, 401

inoculation with SR80 at the time of sowing significantly promoted plant growth and 402

conferred protection against Fp compared with the non-inoculated control (Fig.4a,b,c,d). 403

Within 15 days, plant biomass in both, below-ground (roots, +156%) and above-ground 404

(shoots, +124%), compartments substantially increased by SR80 inoculation (Fig.4b). This is 405

consistent with the observation that the diameter of the stem base was significantly larger at 406

the two time points monitored, although the height of the SR80-inoculated plants was not 407


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larger than the control within the timeframe tested (Fig.4c). Moreover, plant survival rates 408

were significantly higher in the SR80-inoculated group than the untreated group when 409

subjected to Fp infections. The plants in the untreated control all died from Fp infection 410

within 15 days (Fig.4d). qPCR quantification did not reveal a decrease in Fp load after the 411

bacterial inoculation (Fig.4f), which is consistent with our plate assay results. The bacterial 412

communities in soils were profiled at three time points (5, 10 and 15 days). We found that 413

the abundance of the added SR80 in soils gradually decreased to a stable level 10 days after 414

seed germination (~2.4×107 cells g-1 soil) (Fig.4e), in agreement with the relative abundance 415

of SR80 in the soil microbiome continuously declining within the timeframe, from 70.0% to 416

40.74% (Fig.S9). The alpha diversity of soil microbial communities gradually increased in 417

all groups within 15 days, with the highest diversity observed in the uninoculated control 418

(Fig.S10). 419

420

SR80 manipulated plant defense signaling pathways 421

SR80 did not significantly inhibit Fp in soil or on agar plates, indicating that a direct 422

inhibition of the pathogen is not the mechanism for this bacterium to benefit wheat survival 423

and growth. We hypothesized that SR80 modulates expression of genes involved in plant 424

defense. An additional glasshouse experiment was conducted to test this hypothesis, in 425

which plants were inoculated with both the pathogen Fp and the beneficial bacterium SR80 426

and evaluated for expression of marker genes associated with plant defense signaling 427

pathways. We found that when SR80 is present in soils, JA and SA signaling pathways were 428

significantly activated in wheat but only in the presence of Fp. Expression of genes, 429

including TaAOS (+3.1 fold) (Fig.5a), TaNPR1 (+2.2 fold) (Fig.5b), Lipase (+6.0 fold) 430

(Fig.5c), WRKY78 (+3.5 fold) (Fig.5d), PR2 (+3.0 fold) (Fig.5f), and PR3 (+2.3 fold) 431

(Fig.5g), was enhanced by SR80 treatments (Fig.5g). In contrast, expression of PR4 432

marginally decreased by the bacterial treatment without Fp infection. Other PR genes also 433

showed a decrease although were not statistically significant (Fig.5h). 434

435


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Discussion 436

Our study demonstrates that CR disease in wheat plants leads to an enrichment of the 437

beneficial bacterium SR80 in the rhizosphere soil and root endosphere. The assembled SR80 438

was able to significantly enhance plant growth at both the above- and below-ground and 439

induce resistance against the CR disease in glasshouse experiments. Despite strains of 440

S.rhizophila having been shown to suppress mycelial growth in various fungi at times 441

through the production of volatiles (Kai et al., 2007), SR80 did not directly inhibit Fp 442

growth on plates or in soil. However, SR80 can upregulate plant defense signalings (e.g. JA 443

and SA) in shoots with the presence of the pathogen. These findings provide a novel 444

mechanism of tripartite interactions between the devastating fungal pathogen, the plant host 445

and plant-associated microbiota, and revealed a bacterium that may have acted as an early 446

warning system for the onset of plant defense. 447

448

SR80 intimately interacts with plant immune systems and mediates a disease resistance 449

SR80 inoculation tends to suppress the expression of PR-related defense genes in wheat 450

shoots without Fp presence in soils. Consistent with this finding, suppression of the plant 451

root immunity by non-pathogenic Pseudomonas species has recently been observed in 452

Arabidopsis thaliana, which may have facilitated the bacterial colonization on roots (Yu et 453

al., 2019). These suggest that quenching plant immune responses is an emerging strategy for 454

plant-associated bacteria to prevent constitutive activation of plant immune responses. 455

Rhizosphere and endosphere microbiota are rich in microbe-associated molecular patterns 456

(MAMPs), which can trigger the first layer of plant immune defense that restricts pathogen 457

reproduction, MAMP-triggered immunity. SR80 undoubtedly possesses a range of 458

components acting as MAMPs (e.g. flagellin), but how the bacterium avoids eliciting strong 459

immune responses in plants is unclear. Recent conceptual and experimental framework 460

indicates that plant-associated commensal microbes can alleviate/avoid plant immune 461

responses by (i) producing enzymes to scavenge reactive oxygen species (ROS) production 462

of the plant (Sessitsch et al., 2012), (ii) producing organic acids to quench local plant 463


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immune responses (Yu et al., 2019), and (iii) modifying, degrading or changing the structure 464

of MAMPs (Liu et al., 2020). Our whole genome annotation data suggest that SR80 contains 465

multiple genes encoding key components that are functioning by these mechanisms. 466

467

Interestingly, upon challenge with Fp, pre-colonization by SR80 on wheat seedings induced 468

a much stronger plant defense that increased plant survival rates relative to untreated plants. 469

This suggests that SR80 possesses elicitors that triggered Induced Systemic Resistance (ISR) 470

and ‘primed’ the plant for faster and more pronounced responses to pathogen attack. Both 471

the SA and JA signaling pathways of the plant were activated, which is quite unusual 472

because SA and JA signaling pathways are mostly antagonistic, although non-canonical 473

mechanisms of synergism have been reported (Thaler et al., 2012). In monocots, the 474

relationships between the disease signaling pathways and the nutrient acquisition behavior of 475

the pathogen is less understood. 476

477

Fp behaves as a hemi-biotroph as there is an extended initial phase that plants show no 478

symptoms, after which necrotic lesions develop. Two oxalotrophic strains of the same genus 479

as SR80, Stenotrophomonas, were isolated from the tomato rhizosphere and have been 480

shown to upregulate PR-1, a marker gene for the SA pathway (Marina et al., 2019). 481

However, these strains did not influence the expression of PDF1.2, a marker gene for 482

JA/ethylene (ET) signaling pathway (Marina et al., 2019). In line with our findings, a strain 483

of plant growth promoting Stenotrophomonas maltophilia, isolated from the rhizosphere of 484

sorghum, increased synthesis of a range of enzymes associated with defense against fungal 485

pathogens when inoculated on wheat, including peroxidase, β-1,3 glucanase, polyphenol 486

oxidase and phenylalanine ammonia lyase (Singh & Jha, 2017). Overall, our findings 487

suggest that SR80 can play a key role in the three-way interactions with the host plant 488

immunity and the fungal pathogen via a mechanism that enhances the plant defence and 489

growth. 490

491


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SR80 was enriched in root environments upon Fp infection 492

In this study, we used amplicon sequencing and qPCR for the analysis of plant microbiomes, 493

which can detect differences in microbial community structure and estimate the abundance 494

of microbial taxa in soils. Our results revealed that SR80 was thriving at high abundances 495

around roots of the Fp-infected plants (up to 3.7×107 cells g-1 rhizosphere soils). S. 496

maltophilia was also present at high titers in root samples of oilseed rape, about 1.1x107 497

colony forming units (cfu) g-1 wet weight root (Berg et al., 1996). A minimum of 105 cfu g-1 498

root has been reported to be required for the onset of ISR by certain beneficial microbes 499

(Pieterse et al., 2014). Accordingly, the quantity of SR80 accumulated in the rhizosphere and 500

roots of the infected wheat is likely have reached sufficient numbers to induce plant defense 501

responses and confer a protective barrier to restrict Fp. This is consistent with upregulated 502

defenses in wheat plants under both the glasshouse and field conditions by the presence of 503

SR80. However, we noticed that the developed CR symptoms persisted throughout the life 504

cycle of the plant in the field and glasshouse experiments, which suggests that the 505

recruitment of SR80 unlikely cures an existing infection, but may instead increase the plant 506

tolerance to the disease. 507

508

Recent studies in dicot plants including A.thaliana and pepper (Capsicum annuum L. cv. 509

Bukwang) are in line with our findings as attack of foliar tissues by pathogens or insect 510

herbivores resulted in plant-mediated changes in the rhizosphere microbial communities 511

(Kong et al., 2016; Berendsen et al., 2018). Particular microbial taxa affiliated to 512

Stenotrophomonas spp. were similarly enriched in the diseased plants, which suggests that 513

this genus is commonly influenced by different plant biotic stresses. Stenotrophomonas spp. 514

including S. rhizophila possess a strong capacity to colonize root tissues (Hayward et al., 515

2010), which allows the bacterium to intimately interact with the host plant. Under the 516

conditions tested in our study, wheat preferentially selected certain microbial phylotypes (e.g. 517

Gammaproteobacteria) including SR80, resulting in a continuous increase of SR80 518

abundance in the wheat microbiome as habitats shifted from bulk soil to the root endosphere. 519


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In fact, there is evidence to suggest that healthy plants assemble different microbial 520

populations to assist their growth and development (Yuan et al., 2015; Qiao et al., 2017; 521

Imchen et al., 2019). CR disease also modulated the wheat microbiome towards 522

accumulation of more SR80 in the rhizospheric and endophytic microbial communities, 523

suggesting that disease infection can be a critical driver for the plant microbiome assembly, 524

and a cry for help strategy can be triggered to allow plants to actively seek help from soils to 525

cope with biotic stresses. 526

527

It is worth pointing out that not all plant diseases induce microbial changes in the plant 528

microbiome. For example, infection by the necrotrophic pathogen Botrytis cinerea in 529

A.thaliana did not clearly promote microbes in the rhizosphere although it did activate the 530

plant JA-dependent defense pathway (Berendsen et al., 2018). This indicates the pattern of 531

disease-induced changes in the plant microbiome is defined by the particular interactions 532

occurring between a specific plant species and a pathogen. Furthermore, enrichment of 533

particular microbes in plant microbiomes can at times promote the fungal spore germination 534

and virulence (Partida-Martinez & Hertweck, 2005; Seneviratne et al., 2007). 535

Burkholderia spp. for example, forms a symbiotic relationship with the pathogenic fungus 536

Rhizopus, the causative agent of rice seedling blight (Partida-Martinez & Hertweck, 2005). 537

This bacterium produces a toxin that is required for the pathogen to colonize its rice host. In 538

this case, the enrichment of a bacterium helps in the establishment of a fungal disease. 539

540

Collectively, our findings suggest that infection of wheat plants by CR disease results in the 541

recruitment of a beneficial rhizospheric microbe that has the potential to help plant growth 542

and protect plants via modulation of plant defense capacity. The enriched microbe acts as an 543

early warning agent, rapidly activating the JA and SA signaling pathways upon pathogen 544

invasion in plants. This work advances the current understanding of plant-microbe 545

interaction research and supports the coevolution theory of mutualism between the plant and 546

microbes. 547


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548

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Yuan J, Chaparro JM, Manter DK, Zhang R, Vivanco JM, Shen Q. 2015. Roots from 663 distinct plant developmental stages are capable of rapidly selecting their own 664 microbiome without the influence of environmental and soil edaphic factors. Soil 665 Biol Biochem 89: 206-209. 666

667

Acknowledgements 668

The authors would like to acknowledge the financial support from the Australian Research 669

Council (DP1094749; DP170104634; DP190103714). We thank Dr Friday Obanor for 670


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providing us Fp strains and Dr Anna Balzer for helping with plant sampling and soil 671

collection. We also thank Associate Professor Mark Dieters for providing wheat seeds and 672

Dr Laura E. Brettell for proofreading this article. 673

674

Author contributions 675

H.L., P.S., L.C.C conceptualized the idea, which was further refined by B.K.S; H.L., L.C.C., 676

and C.P. did the plant and soil sampling; H.L. and J.L. processed the plant and soil samples 677

and did the measurements for glasshouse treatments; H.L. analyzed the data and wrote the 678

first draft with significant inputs from B.K.S; all authors have critically read and revised the 679

manuscript. 680

681

Data availability 682

Data of this study are available at 10.6084/m9.figshare.12464465. Other relevant data are 683

available upon request. 684

685

Figure captions 686

Fig.1 The effects of Fp-infection on wheat stem and expression of defense genes. An 687

example of healthy and Fp-infected wheat stems (internode 1) (a). Fp-infected wheat stems 688

had a brown discoloration (relative abundance of Fp≥ 1) while the healthy stems were 689

white/light green (Fp abundance< 1). A Pearson correlation of Fp abundance with visually 690

rated disease levels at stem base (b). Effects of Fp infection on the transcription of ten genes 691

associated with jasmonic acid (JA) and salicylic acid (SA) signaling pathways in wheat (c-l). 692

Linear correlation tests were performed for these defense genes with the Fp load present in 693

the stem base. Each grey circle represents an independent measurement (n = 58). Red dashes 694

show significant regression and the overlaid shaded area represents 95% confidence intervals. 695

Both the JA and SA signaling pathways were activated by the Fp infection (m), and a 696

heatmap summarizing the correlation of the expression of defense genes in leaves with the 697

disease severity in wheat (n). 698


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699

Fig.2 Effects of Fp infection on wheat-associated microbial communities. Redundancy 700

anaysis sumarizing variations in composition of microbial communities in the rhizosphere 701

soil (a) and root endosphere (b) attributed to crown rot. Grey crosses shown in (a) and (b) 702

represent bacterial OTUs detected in the rhizosphere and root endosphere. Pearson 703

correlations of the SR80 abundance in the rhizosphere soil (c) and root endosphere (d) with 704

Fp abundance in wheat stems. Gradient increases in relative abundance of SR80 from the 705

bulk soil to the rhizosphere, and to the root endosphere (e). A table summarizing the 706

correlation of SR80 abundances with defence gene expression in leaves (f). Asterisks 707

indicate significant correlations (* P�<�0.05, ** P�<�0.01, *** P�<�0.001). 708

709

Fig.3 Morphology of SR80 isolated from wheat rhizosphere soil and root endosphere. 710

Colony morphology of SR80 grown for 24 h on trypticase soy agar (TSA) (a). Bacterial cell 711

morphology under a light microscope (b). Slight inhibition of the bacterium on Fp growth on 712

a dual media (1/2 PDA+1/2 TSA) (c). Bacteria used as positive controls at the bottom right 713

were two strains of Burkholderia spp. 714

715

Fig.4 Effects of SR80 inoculation on wheat growth and survival. Wheat phenotypes 14 days 716

post treatment applications (a). Control: no inoculation, SR80: inoculation with SR80 only, 717

Fp: inoculation with Fp only, SR80+Fp: dual inoculation with SR80 and Fp. Biomass 718

accumulation of wheat shoots and roots 15 days after the treatment applications (b). Increase 719

in plant height and stem size over 15 days from the application of treatments (c). Wheat 720

survival rates under different treatments (d). Changes in abundance of SR80 (e) and Fp (f) 721

abundance in soils. Asterisks indicate significant differences between treatments 722

(*P�<�0.05, **P�<�0.01, ***P�<�0.001). Error bars in (b)- (f) represent standard errors 723

of the mean (n=6). 724

725


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Fig.5 Effects of SR80 and Fp inoculations on the transcription of genes associated with JA 726

and SA signaling pathways. Glasshouse experiment 1 (left) and 2 (right) were separated by 727

black dash lines on each graph. Asterisks indicate significant differences between treatments 728

(*P�<�0.05, **P�<�0.01, ***P�<�0.001). Error bars represent standard errors of the 729

means (n =�6). 730

731

Fig.6 Schematic drawing illustrating biological implications of SR80 on plant growth and 732

defense. The bacterium SR80 can modulate wheat growth and defense, which seems to be 733

mediated by the plant immune system. The plant favors the enrichment of the bacterium 734

from the rhizosphere soils and to the root endosphere. Moreover, when exposed to Fp, the 735

wheat plant favors the enrichment with even more SR80 in the rhizosphere. Such an active 736

recruitment process is accompanied by an enhanced defense gene expression in leaves. 737

Future research can investigate (i) whether plant leaves enrich the bacterium (process 1), and 738

(ii) whether allelopathic effects lead to the enrichment of the bacterium in the neighboring 739

threatened plants (process 2&3). 740


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Evidence for the plant recruitment of beneficial microbes ... · 31/07/2020 · 4 Hongwei Liu1, 2, Jiayu Li1, Lilia C. Cavalhais3, Cassandra Percy4, Jay Prakash Verma5, Peer 5 M